1 Setup

setwd("/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/Conditions")
suppressPackageStartupMessages({
    library(data.table)
    library(DESeq2)
    library(gplots)
    library(here)
    library(hyperSpec)
    library(limma)
    library(LSD)
    library(magrittr)
    library(matrixStats)
    library(parallel)
    library(pander)
    library(plotly)
    library(RColorBrewer)
    library(scatterplot3d)
    library(tidyverse)
    library(tximport)
    library(VennDiagram)
    library(vsn)
})
suppressPackageStartupMessages({
    source("~/Git/UPSCb/UPSCb-common/src/R/featureSelection.R")
    source("~/Git/UPSCb/UPSCb-common/src/R/gopher.R")
    source("~/Git/UPSCb/UPSCb-common/src/R/plot.multidensity.R")
    source("~/Git/UPSCb/UPSCb-common/src/R/volcanoPlot.R")
})
lfc <- 0.5
FDR <- 0.01
pal <- c(brewer.pal(8,"Dark2"),1)
pal2 <- brewer.pal(9,"Paired") #require package RColorBrewer
cols <- rainbow(17)
hpal <- colorRampPalette(c("blue","white","red"))(100)
mar <- par("mar")

2 Raw data

2.1 Loading of sample information

  • Read the sample information
samples <- read.csv("~/Git/arabidopsis-nutrition-tor/doc/samples3.csv")
  • Remove unnecessary samples
samples %<>% filter(!grepl("P11554_1",SciLifeID)) %>% 
    filter(! SciLifeID %in% c("P13406_101",
                        "P14066_128",
                        "P14066_133",
                        "P13406_102",
                        "P14066_131")) %>%
    filter(! Nutrition == "PKS") %>%
    mutate(Nutrition=relevel(as.factor(Nutrition),"NPS"),AZD=relevel(as.factor(AZD),"DMSO"))

samples <- samples[order(samples$Timepoint, samples$Nutrition, samples$AZD),]

samples %<>% mutate(Timepoint,Timepoint=factor(paste0("T",Timepoint)))

2.1.1 Load the data

  • Call the data
filenames <- list.files("../Salmon", 
                    recursive = TRUE, 
                    pattern = "quant.sf",
                    full.names = TRUE)
  • Name the data
names(filenames) <- sub("_S.*","",sapply(strsplit(filenames, "/"), .subset, 3))
  • Match data <=> sample list
filenames <- filenames[match(samples$SciLifeID,names(filenames))]
filenames <-filenames[!is.na(names(filenames))]
samples <- samples[match(names(filenames),samples$SciLifeID),]
  • Annotate the samples
samples$Conditions <- factor(paste(samples$Timepoint,
                                   samples$Nutrition,
                                   samples$AZD,sep="_"),
                             levels=c("T0_T0_0",
                                      "T6_NPS_DMSO", "T6_NPS_AZD", "T6_NS_DMSO", "T6_NS_AZD", "T6_NP_DMSO", "T6_NP_AZD",
                                      "T24_NPS_DMSO", "T24_NPS_AZD", "T24_NS_DMSO", "T24_NS_AZD", "T24_NP_DMSO", "T24_NP_AZD"))
samples <- cbind(samples,
                 Id = gsub(".+-",
                           "",
                           samples$SampleName))
samples <- cbind(samples,
                 Tp_Id = factor(paste(samples$Timepoint,
                                      samples$Id,
                                      sep=".")))
write.csv(samples,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/samplelist.csv")

3 Expression data

Read the expression at the transcript level

tx <- suppressMessages(tximport(files = filenames, 
                                type = "salmon", 
                                txOut = TRUE))

summarise to genes

tx2gene <- data.frame(TXID=rownames(tx$counts),
                      GENEID=sub("\\.[0-9]+","",rownames(tx$counts)))
gx <- summarizeToGene(tx,tx2gene=tx2gene)
## summarizing abundance
## summarizing counts
## summarizing length
kg <- round(gx$counts) 

Sanity check

stopifnot(all(colnames(kg) == samples$SciLifeID))

3.1 Raw data export

#dir.create(file.path("analysis_Tom","salmon"),showWarnings=FALSE,recursive=TRUE)
#write.table(kg,file="/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/nutrition-unormalised-gene-expression_data.csv")
#save(kg, samples, file = "/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/counts.rda")

3.2 Preliminary validations

3.2.1 Check for the genes that are never expressed

sel <- rowSums(kg) == 0 
sprintf("%s%% (%s) of %s genes are not expressed",
        round(sum(sel) * 100/ nrow(kg),digits=1),
        sum(sel),
        nrow(kg))
## [1] "17.9% (5793) of 32310 genes are not expressed"

4 Data normalisation

For visualization, the data is submitted to a variance stabilization transformation using DESeq2. The dispersion is estimated independently of the sample type

dds <- DESeqDataSetFromMatrix(
    countData = kg,
    colData = samples,
    design = ~ Conditions)
## converting counts to integer mode
dds <- estimateSizeFactors(dds)

4.1 Perform a Variance Stabilizing Transformation for plotting

vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)

Write out

stopifnot(all(colnames(vsd) == samples$SciLifeID))
colnames(vsd) <- samples$Tp_Id
write.csv(vsd,"/mnt/picea/projects/arabidopsis/jhanson/arabidopsis-nutrition-TOR/analysis_Tom/library-size-normalized_variance-stabilized_data_nutrition.csv")

5 Multivariate analysis

5.1 PCA

Principal Component Analysis on the normalized data * Establishment of the PCA

conditions1 <- factor(paste(samples$AZD,samples$Nutrition,sep="_"))
pc <- prcomp(t(vsd))
percent <- round(summary(pc)$importance[2,]*100);percent
##  PC1  PC2  PC3  PC4  PC5  PC6  PC7  PC8  PC9 PC10 PC11 PC12 PC13 PC14 PC15 PC16 
##   43   24   13    6    4    2    1    1    1    1    0    0    0    0    0    0 
## PC17 PC18 PC19 PC20 PC21 PC22 PC23 PC24 PC25 PC26 PC27 PC28 PC29 PC30 PC31 PC32 
##    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0 
## PC33 PC34 PC35 PC36 PC37 PC38 PC39 PC40 PC41 PC42 PC43 PC44 
##    0    0    0    0    0    0    0    0    0    0    0    0
  • Graphical representation of PC1 x PC2
conds <- droplevels(conditions1)
plot(pc$x[,1],
     pc$x[,2],
     xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
     ylab=paste("Comp. 2 (",percent[2],"%)",sep=""),
     col=pal[as.integer(conds)],
     pch=c(15,16,17)[as.factor(samples$Timepoint)],
     main="All timepoints")

legend("bottomright",pch=19,
       col=pal[1:nlevels(conds)],
       legend=levels(conds))

legend("topleft",pch=c(15,16,17),
       col="black",
       legend=c("T0","T6","T24"))

  • Graphical representation of PC2 x PC3
plot(pc$x[,2],
     pc$x[,3],
     xlab=paste("Comp. 2 (",percent[2],"%)",sep=""),
     ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
     col=pal[as.integer(conds)],
     pch=c(15,16,17)[as.factor(samples$Timepoint)],
     main="All timepoints")

legend("bottomleft",pch=19,
       col=pal[1:nlevels(conds)],
       legend=levels(conds))

legend("topleft",pch=c(15,16,17),
       col="black",
       legend=c("T0","T6","T24"))

  • Graphical representation of PC1 x PC3
plot(pc$x[,1],
     pc$x[,3],
     xlab=paste("Comp. 1 (",percent[1],"%)",sep=""),
     ylab=paste("Comp. 3 (",percent[3],"%)",sep=""),
     col=pal[as.integer(conds)],
     pch=c(15,16,17)[as.factor(samples$Timepoint)],
     main="All timepoints")

legend("bottomleft",pch=19,
       col=pal[1:nlevels(conds)],
       legend=levels(conds))

legend("bottomright",pch=c(15,16,17),
       col="black",
       legend=c("T0","T6","T24"))

6 Differential expression compared to T0

6.1 Filtration of samples based on timepoint

sel <- samples$Timepoint %in% c("T0","T6","T24")
suppressMessages(dds <- DESeqDataSetFromMatrix(
    countData = kg[,sel],
    colData = samples[sel,],
    design = ~ Conditions))

6.2 Differential expression analysis

dds <- DESeq(dds)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing

6.3 Variance Stabilising Transformation

6.3.1 Perform a Variance Stabilizing Transformation for plotting

vst <- varianceStabilizingTransformation(dds,blind=FALSE)
vsd <- assay(vst)
vsd <- vsd - min(vsd)

The contrast by default is the first one (not Intercept)

resultsNames(dds)
##  [1] "Intercept"                          "Conditions_T6_NPS_DMSO_vs_T0_T0_0" 
##  [3] "Conditions_T6_NPS_AZD_vs_T0_T0_0"   "Conditions_T6_NS_DMSO_vs_T0_T0_0"  
##  [5] "Conditions_T6_NS_AZD_vs_T0_T0_0"    "Conditions_T6_NP_DMSO_vs_T0_T0_0"  
##  [7] "Conditions_T6_NP_AZD_vs_T0_T0_0"    "Conditions_T24_NPS_DMSO_vs_T0_T0_0"
##  [9] "Conditions_T24_NPS_AZD_vs_T0_T0_0"  "Conditions_T24_NS_DMSO_vs_T0_T0_0" 
## [11] "Conditions_T24_NS_AZD_vs_T0_T0_0"   "Conditions_T24_NP_DMSO_vs_T0_T0_0" 
## [13] "Conditions_T24_NP_AZD_vs_T0_T0_0"

6.3.2 Effect of 6 hrs of treatment

res <- results(dds,name = "Conditions_T6_NPS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9664 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5302 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4362 genes that are repressed
res <- results(dds,name = "Conditions_T6_NPS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NPS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8735 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4639 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4096 genes that are repressed
res <- results(dds,name = "Conditions_T6_NS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 6589 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3553 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3036 genes that are repressed
res <- results(dds,name = "Conditions_T6_NS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9218 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4775 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4443 genes that are repressed
res <- results(dds,name = "Conditions_T6_NP_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9491 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5053 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4438 genes that are repressed
res <- results(dds,name = "Conditions_T6_NP_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T6_NP_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7818 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4332 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3486 genes that are repressed

6.3.3 Effect of 24 hrs of treatment

res <- results(dds,name = "Conditions_T24_NPS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 10531 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 5150 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 5381 genes that are repressed
res <- results(dds,name = "Conditions_T24_NPS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NPS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8349 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4066 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4283 genes that are repressed
res <- results(dds,name = "Conditions_T24_NS_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 4579 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 2165 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 2414 genes that are repressed
res <- results(dds,name = "Conditions_T24_NS_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NS_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 7102 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 3258 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 3844 genes that are repressed
res <- results(dds,name = "Conditions_T24_NP_DMSO_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_DMSO_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 9502 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4685 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4817 genes that are repressed
res <- results(dds,name = "Conditions_T24_NP_AZD_vs_T0_T0_0")
data <- data.frame(rownames(res), res$log2FoldChange, res$padj)
write.table(data, file = "Conditions_T24_NP_AZD_vs_T0_T0_0.csv", sep = ";", row.names = FALSE, dec=",")
cutoffs <- abs(res$log2FoldChange) >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff1 <- res$log2FoldChange >= lfc & ! is.na(res$padj) & res$padj <= FDR
cutoff2 <- res$log2FoldChange <= -lfc & ! is.na(res$padj) & res$padj <= FDR

message(sprintf("There are %s genes that are differentially expressed",sum(cutoffs)))
## There are 8906 genes that are differentially expressed
message(sprintf("There are %s genes that are induced",sum(cutoff1)))
## There are 4614 genes that are induced
message(sprintf("There are %s genes that are repressed",sum(cutoff2)))
## There are 4292 genes that are repressed

7 Expression level analysis of specific gene lists

levels(samples$Conditions)
##  [1] "T0_T0_0"      "T6_NPS_DMSO"  "T6_NPS_AZD"   "T6_NS_DMSO"   "T6_NS_AZD"   
##  [6] "T6_NP_DMSO"   "T6_NP_AZD"    "T24_NPS_DMSO" "T24_NPS_AZD"  "T24_NS_DMSO" 
## [11] "T24_NS_AZD"   "T24_NP_DMSO"  "T24_NP_AZD"
sel_T0 <- samples$Timepoint %in% c("T0","T6","T24")

suppressMessages(dds_T0 <- DESeqDataSetFromMatrix(
    countData = kg[,sel_T0],
    colData = samples[sel_T0,],
    design = ~ Conditions))

7.1 Differential expression analysis

dds_T0 <- DESeq(dds_T0)
## estimating size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 2 genes
## -- DESeq argument 'minReplicatesForReplace' = 7 
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing

7.2 Variance Stabilising Transformation

7.2.1 Perform a Variance Stabilizing Transformation for plotting

vst_T0 <- varianceStabilizingTransformation(dds_T0,blind=FALSE)
vsd_T0 <- assay(vst_T0)
vsd_T0 <- vsd_T0 - min(vsd_T0)

7.3 Export the complete list of averages and SDs

sel1 <- rownames(vsd_T0)
expr <- vsd_T0[match(sel1,rownames(vsd_T0)),]
Avg <- sapply(split.data.frame(t(expr),
                               f = droplevels(samples$Conditions[sel_T0])),
              colMeans)
SD <- sapply(split.data.frame(t(expr),f = droplevels(samples$Conditions[sel_T0])),colSds)
rownames(SD) <- rownames(Avg)
write.table(Avg, file = "Averaged_Normalized_Counts.csv", sep = ";", row.names = FALSE, dec=",")
write.table(rownames(Avg), file = "Averaged_Normalized_Counts_genes.csv", sep = ";", row.names = FALSE, dec=",")

7.4 TOR complex members

7.4.1 Preparation of the complex member list

sel1 <- c("AT1G50030","AT3G18140","AT2G22040","AT3G08850","AT5G01770") 

7.4.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.4.3 Graphical representations

7.4.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

7.4.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
    barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
    arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

7.4.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
    plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
         xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
    axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
    arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
           y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

7.4.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
    a[1:6,1] <- AvgTOR[i,1]
    a[1:6,2] <- AvgTOR[i,2:7]
    a[1:6,3] <- AvgTOR[i,8:13]
    
    b[1:6,1] <- SDTOR[i,1]
    b[1:6,2] <- SDTOR[i,2:7]
    b[1:6,3] <- SDTOR[i,8:13]
    
    plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
    lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
    lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
    lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
    lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
    lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
    
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[1,] - b[1,],
           y1=a[1,] + b[1,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[2,] - b[2,],
           y1=a[2,] + b[2,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[3,] - b[3,],
           y1=a[3,] + b[3,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[4,] - b[4,],
           y1=a[4,] + b[4,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[5,] - b[5,],
           y1=a[5,] + b[5,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[6,] - b[6,],
           y1=a[6,] + b[6,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

7.4.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

7.4.4 Graphical representations of all the samples

7.4.4.1 Preparation of the sample data

sel1 <- c("AT1G50030","AT3G18140","AT3G08850","AT5G01770")
AvgTOR <- Avg[match(sel1,rownames(Avg)),]
TOR <- vsd_T0[match(sel1,rownames(vsd_T0)),]
TOR_norm <- TOR/AvgTOR[,1]
TOR_norm <- log2(TOR_norm)
colnames(TOR_norm) <- samples$Conditions


a <- match(colnames(TOR_norm),samples$Conditions)
plot(TOR_norm[4,] ~ a, ylim=c(-0.5,0.5),main="AT5G01770")
b <- c(1,9,12,21,24,15,18,27,30,39,42,33,36)
lines(b,AvgTOR_norm[5,])

7.5 Genes involved in the cell cycle

7.5.1 Preparation of a list of genes of the cell cycle

sel1 <- read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,1]

7.6 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.6.1 Graphical representations

7.6.1.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

7.6.1.2 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
    plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
         xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
    axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
    arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
           y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

7.6.1.3 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
    {
    a[1:6,1] <- AvgTOR[i,1]
    a[1:6,2] <- AvgTOR[i,2:7]
    a[1:6,3] <- AvgTOR[i,8:13]
    
    b[1:6,1] <- SDTOR[i,1]
    b[1:6,2] <- SDTOR[i,2:7]
    b[1:6,3] <- SDTOR[i,8:13]
    
    plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
    lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
    lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
    lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
    lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
    lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
    
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[1,] - b[1,],
           y1=a[1,] + b[1,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[2,] - b[2,],
           y1=a[2,] + b[2,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[3,] - b[3,],
           y1=a[3,] + b[3,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[4,] - b[4,],
           y1=a[4,] + b[4,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[5,] - b[5,],
           y1=a[5,] + b[5,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[6,] - b[6,],
           y1=a[6,] + b[6,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

7.6.1.4 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])

AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3

heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,8),
          labRow = read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,2])

heatmap.2(AvgTOR_norm,
          trace="none",
          col=hpal,
          Colv=FALSE,
          dendrogram = "row",
          labRow = read.csv("~/arabidopsis-nutrition-TOR/seidr/cell_cycle_genes.csv", sep=";")[,2],
          margins=c(8,8),
          hclustfun = function(X){hclust(X,method="ward.D2")})

7.7 Histone genes

7.7.1 List of Histone H3 family members excluding the “AT1G75610” which was not detected and the “AT1G19890” which was found detected only in the T0 sample

sel1 <- c("AT5G65360","AT1G09200","AT3G27360","AT5G10400","AT5G65350","AT5G10390","AT4G40030",
          "AT4G40040","AT5G10980","AT1G13370","AT1G75600","AT1G01370") 

7.7.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.7.3 Graphical representations

7.7.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)

7.7.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
    barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
    arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.2,code=3)
}

7.7.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
    plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
         xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
    axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
    arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
           y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.05,code=3)
}

7.7.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
    a[1:6,1] <- AvgTOR[i,1]
    a[1:6,2] <- AvgTOR[i,2:7]
    a[1:6,3] <- AvgTOR[i,8:13]
    
    b[1:6,1] <- SDTOR[i,1]
    b[1:6,2] <- SDTOR[i,2:7]
    b[1:6,3] <- SDTOR[i,8:13]
    
    plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
    lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
    lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
    lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
    lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
    lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
    
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[1,] - b[1,],
           y1=a[1,] + b[1,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[2,] - b[2,],
           y1=a[2,] + b[2,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[3,] - b[3,],
           y1=a[3,] + b[3,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[4,] - b[4,],
           y1=a[4,] + b[4,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[5,] - b[5,],
           y1=a[5,] + b[5,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[6,] - b[6,],
           y1=a[6,] + b[6,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

7.7.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

7.8 Genes involved in the response to phosphate starvation

7.8.1 Preparation of the transporter list (Poirier and Bucher, 2002) and phosphatases (Hanchi, PhD thesis) and Pi starvation responsive genes (Wang et al., 2018, Front. Plant Sci.)

sel1 <- c("AT5G43350","AT5G43370","AT5G43360","AT2G38940","AT2G32830","AT5G43340","AT3G54700",
          "AT1G20860","AT1G76430","AT3G26570","AT5G14040","AT3G48850","AT2G17270","AT5G46110",
          "AT5G33320","AT5G54800","AT1G61800","AT5G17640","AT1G73010","AT1G17710",
          "AT3G09922" ,"AT2G02990","AT3G17790") 

sel1 <- c("AT5G43350","AT5G43370","AT5G43360","AT2G38940","AT2G32830","AT5G43340","AT3G54700",
          "AT1G20860","AT1G76430","AT3G26570","AT5G14040","AT3G48850","AT2G17270","AT5G46110",
          "AT5G33320","AT5G54800","AT1G61800","AT5G17640","AT1G73010","AT1G17710") 

7.8.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.8.3 Graphical representations

7.8.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

7.8.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
    barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
    arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

7.8.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
    plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
         xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
    axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
    arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
           y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

7.8.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
    a[1:6,1] <- AvgTOR[i,1]
    a[1:6,2] <- AvgTOR[i,2:7]
    a[1:6,3] <- AvgTOR[i,8:13]
    
    b[1:6,1] <- SDTOR[i,1]
    b[1:6,2] <- SDTOR[i,2:7]
    b[1:6,3] <- SDTOR[i,8:13]
    
    plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
    lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
    lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
    lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
    lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
    lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
    
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[1,] - b[1,],
           y1=a[1,] + b[1,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[2,] - b[2,],
           y1=a[2,] + b[2,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[3,] - b[3,],
           y1=a[3,] + b[3,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[4,] - b[4,],
           y1=a[4,] + b[4,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[5,] - b[5,],
           y1=a[5,] + b[5,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[6,] - b[6,],
           y1=a[6,] + b[6,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

7.8.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

7.8.4 Preparation of the systemically-regulated genes by Pi starvation (Thibaud et al., 2010)

sel1 <- c('AT5G01220','AT3G02870','AT3G17790','AT5G64000','AT3G52820','AT2G11810','AT1G73010',
          'AT3G03540','AT3G02040','AT5G20410','AT3G05630','AT4G33030','AT2G27190','AT4G00550',
          'AT2G45130','AT5G20150','AT2G26660','AT1G68740','AT2G32830','AT2G38940','AT1G20860',
          'AT3G58810','AT5G56080','AT5G04950','AT1G23020','AT4G19690','AT3G46900','AT4G19680',
          'AT1G09790','AT3G58060','AT5G03570','AT2G28160','AT2G03260','AT1G74770','AT4G09110',
          'AT5G06490','AT1G49390','AT1G72200','AT2G35000','AT3G12900','AT4G30120') 

7.8.5 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.8.6 Graphical representations

7.8.6.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

7.8.6.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
    barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
    arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

7.8.6.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
    plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
         xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
    axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
    arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
           y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

7.8.6.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
    a[1:6,1] <- AvgTOR[i,1]
    a[1:6,2] <- AvgTOR[i,2:7]
    a[1:6,3] <- AvgTOR[i,8:13]
    
    b[1:6,1] <- SDTOR[i,1]
    b[1:6,2] <- SDTOR[i,2:7]
    b[1:6,3] <- SDTOR[i,8:13]
    
    plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
    lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
    lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
    lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
    lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
    lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
    
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[1,] - b[1,],
           y1=a[1,] + b[1,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[2,] - b[2,],
           y1=a[2,] + b[2,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[3,] - b[3,],
           y1=a[3,] + b[3,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[4,] - b[4,],
           y1=a[4,] + b[4,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[5,] - b[5,],
           y1=a[5,] + b[5,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[6,] - b[6,],
           y1=a[6,] + b[6,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[1, ] - b[1, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[2, ] - b[2, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[5, ] - b[5, : zero-
## length arrow is of indeterminate angle and so skipped
## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[6, ] - b[6, : zero-
## length arrow is of indeterminate angle and so skipped

7.8.6.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

7.9 Genes deregulated in Nicolai et al., 2006

7.9.1 List of the genes

sel1 <- c('AT2G03090','AT3G10950','AT3G25250','AT4G30280','AT5G13210','AT5G65110','AT1G12780','AT4G02520','AT3G12970','AT3G47540',
          'AT4G11650','AT4G30490','AT2G29490','AT2G38870','AT3G45970','AT5G22920','AT5G39320','AT1G75380','AT5G39580','AT5G57655',
          'AT1G54100','AT1G68440','AT1G76870','AT2G33150','AT3G04720','AT3G44300','AT3G59270','AT1G51400','AT2G30860','AT3G28180',
          'AT4G37610','AT5G07440','AT5G49360') 

7.9.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.9.3 Graphical representations

7.9.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1)
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)
## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR - SDTOR, : zero-
## length arrow is of indeterminate angle and so skipped

7.9.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
    barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i], las=2)
    arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.2,code=3)
}

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = barcenters, x1 = barcenters, y0 = AvgTOR[i, ] -
## SDTOR[i, : zero-length arrow is of indeterminate angle and so skipped

7.9.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
    plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
         xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
    axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
    arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
           y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
           lwd=1.5, angle=90, length=0.05,code=3)
}

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = 1:length(AvgTOR[i, ]), x1 = 1:length(AvgTOR[i, ]), :
## zero-length arrow is of indeterminate angle and so skipped

7.9.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
    a[1:6,1] <- AvgTOR[i,1]
    a[1:6,2] <- AvgTOR[i,2:7]
    a[1:6,3] <- AvgTOR[i,8:13]
    
    b[1:6,1] <- SDTOR[i,1]
    b[1:6,2] <- SDTOR[i,2:7]
    b[1:6,3] <- SDTOR[i,8:13]
    
    plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
    lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
    lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
    lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
    lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
    lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
    
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[1,] - b[1,],
           y1=a[1,] + b[1,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[2,] - b[2,],
           y1=a[2,] + b[2,],
           lwd=1, angle=90, length=0.05, code=3)
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[3,] - b[3,],
           y1=a[3,] + b[3,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[4,] - b[4,],
           y1=a[4,] + b[4,],
           lwd=1, angle=90, length=0.05, code=3, col="turquoise")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[5,] - b[5,],
           y1=a[5,] + b[5,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
    arrows(x0=c(0,6,24),
           x1=c(0,6,24),
           y0=a[6,] - b[6,],
           y1=a[6,] + b[6,],
           lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[4, ] - b[4, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

## Warning in arrows(x0 = c(0, 6, 24), x1 = c(0, 6, 24), y0 = a[3, ] - b[3, : zero-
## length arrow is of indeterminate angle and so skipped

7.9.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -3] <- -3; AvgTOR_norm[AvgTOR_norm > 3] <- 3


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

7.10 Proteasome

7.10.1 List of genes coding for the 19S proteasome

sel1 <- c("AT1G04810","AT1G09100","AT1G45000","AT1G53750","AT1G64520","AT2G20140","AT2G20580",
          "AT2G32730","AT3G05530","AT4G19006","AT4G24820","AT4G28470","AT4G29040","AT4G38630",
          "AT5G05780","AT5G09900","AT5G19990","AT5G20000","AT5G43010","AT5G45620","AT5G58290",
          "AT5G64760") 

7.10.2 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.10.3 Graphical representations

7.10.3.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)

7.10.3.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

7.10.3.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

7.10.3.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

7.10.3.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="row",
          trace="none",
          Colv=FALSE,
          margins=c(8,12),
          hclustfun = function(X){hclust(X,method="ward.D2")})

7.10.4 List of genes coding for the 20S proteasome

sel1 <- c("AT1G13060","AT1G16470","AT1G21720","AT1G47250","AT1G53850","AT1G56450","AT1G77440",
          "AT2G05840","AT2G27020","AT3G14290","AT3G22110","AT3G22630","AT3G27430","AT3G51260",
          "AT3G60820","AT4G14800","AT4G31300","AT5G35590","AT5G40580","AT5G66140") 

7.10.5 Preparation of the expression table for the shortlisted genes

AvgTOR <- Avg[match(sel1,rownames(Avg)),]
SDTOR <- SD[match(sel1,rownames(SD)),]

7.10.6 Graphical representations

7.10.6.1 Combined barplots

barcenters <- barplot(AvgTOR,beside=T, cex.names=0.7,legend.text = sel1,ylim=c(0,4))
arrows(x0=barcenters, x1=barcenters, y0=AvgTOR-SDTOR, y1=AvgTOR+SDTOR,
       lwd=1.5, angle=90, length=0.05,code=3)

7.10.6.2 Separated barplots

for (i in 1:length(AvgTOR[,1])){
  barcenters <- barplot(AvgTOR[i,],beside=T, cex.names=0.7,legend.text = sel1[i],ylim=c(0,4))
  arrows(x0=barcenters, x1=barcenters, y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.2,code=3)
}

7.10.6.3 Individual graphs without colors

for (i in 1:length(AvgTOR[,1]))
{
  plot(AvgTOR[i,],ylim=c(min(AvgTOR[i,]-SDTOR[i,]),max(AvgTOR[i,]+SDTOR[i,])),
       xaxt="n",xlab="",ylab=sprintf("gene = %s",rownames(AvgTOR)[i]))
  axis(side = 1,at=1:13, colnames(AvgTOR),cex.axis=0.7,las=2)
  arrows(x0=1:length(AvgTOR[i,]), x1=1:length(AvgTOR[i,]),
         y0=AvgTOR[i,]-SDTOR[i,], y1=AvgTOR[i,]+SDTOR[i,],
         lwd=1.5, angle=90, length=0.05,code=3)
}

7.10.6.4 Individual graphs with colors

a <- matrix(NA, nrow=6, ncol=3)
colnames(a) <- c(0,6,24)
rownames(a) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")
b <- matrix(NA, nrow=6, ncol=3)
colnames(b) <- c(0,6,24)
rownames(b) <- c("NPS_DMSO","NPS_AZD","NS_DMSO","NS_AZD","NP_DMSO","NP_AZD")


for (i in 1:length(AvgTOR[,1]))
{
  a[1:6,1] <- AvgTOR[i,1]
  a[1:6,2] <- AvgTOR[i,2:7]
  a[1:6,3] <- AvgTOR[i,8:13]
  
  b[1:6,1] <- SDTOR[i,1]
  b[1:6,2] <- SDTOR[i,2:7]
  b[1:6,3] <- SDTOR[i,8:13]
  
  plot(colnames(a),a[1,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),ylab=rownames(AvgTOR)[i])
  lines(colnames(a),a[2,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),lty=2)
  lines(colnames(a),a[3,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise")
  lines(colnames(a),a[4,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="turquoise",lty=2)
  lines(colnames(a),a[5,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3")
  lines(colnames(a),a[6,], type="l",ylim=c(min(a)-max(b),max(a)+max(b)),col="hotpink3",lty=2)
  
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[1,] - b[1,],
         y1=a[1,] + b[1,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[2,] - b[2,],
         y1=a[2,] + b[2,],
         lwd=1, angle=90, length=0.05, code=3)
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[3,] - b[3,],
         y1=a[3,] + b[3,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[4,] - b[4,],
         y1=a[4,] + b[4,],
         lwd=1, angle=90, length=0.05, code=3, col="turquoise")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[5,] - b[5,],
         y1=a[5,] + b[5,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
  arrows(x0=c(0,6,24),
         x1=c(0,6,24),
         y0=a[6,] - b[6,],
         y1=a[6,] + b[6,],
         lwd=1, angle=90, length=0.05, code=3, col="hotpink3")
}

7.10.6.5 Heatmap

AvgTOR[AvgTOR == 0] <- 0.000001
AvgTOR_norm <- log2(AvgTOR[,] / AvgTOR[,1])
AvgTOR_norm[AvgTOR_norm < -0.5] <- -0.5; AvgTOR_norm[AvgTOR_norm > 0.5] <- 0.5


heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="none",
          trace="none",
          Colv=FALSE,
          Rowv=FALSE,
          margins=c(8,12))

heatmap.2(AvgTOR_norm,
          col=hpal,
          dendrogram="row",
          trace="none",
          Colv=FALSE,
          margins=c(8,12),
          hclustfun = function(X){hclust(X,method="ward.D2")})

7.11 Preparation of other lists

  • Preparation of the hexokinase list
sel1 <- c("AT1G05205","AT1G47840","AT1G47845","AT2G19860","AT4G29130")
  • Preparation of the AtHXK1
sel1 <- c("AT1G47845","AT4G29130")

8 Session Info

## R version 4.0.3 (2020-10-10)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 18.04.5 LTS
## 
## Matrix products: default
## BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so
## 
## locale:
##  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
##  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
##  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
##  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
##  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
## 
## attached base packages:
##  [1] grid      parallel  stats4    stats     graphics  grDevices utils    
##  [8] datasets  methods   base     
## 
## other attached packages:
##  [1] vsn_3.58.0                  VennDiagram_1.6.20         
##  [3] futile.logger_1.4.3         tximport_1.18.0            
##  [5] forcats_0.5.0               stringr_1.4.0              
##  [7] dplyr_1.0.2                 purrr_0.3.4                
##  [9] readr_1.4.0                 tidyr_1.1.2                
## [11] tibble_3.0.4                tidyverse_1.3.0            
## [13] scatterplot3d_0.3-41        RColorBrewer_1.1-2         
## [15] plotly_4.9.2.1              pander_0.6.3               
## [17] magrittr_2.0.1              LSD_4.1-0                  
## [19] limma_3.46.0                hyperSpec_0.99-20200527    
## [21] xml2_1.3.2                  ggplot2_3.3.2              
## [23] lattice_0.20-41             here_1.0.0                 
## [25] gplots_3.1.0                DESeq2_1.30.0              
## [27] SummarizedExperiment_1.20.0 Biobase_2.50.0             
## [29] MatrixGenerics_1.2.0        matrixStats_0.57.0         
## [31] GenomicRanges_1.42.0        GenomeInfoDb_1.26.1        
## [33] IRanges_2.24.0              S4Vectors_0.28.0           
## [35] BiocGenerics_0.36.0         data.table_1.13.2          
## 
## loaded via a namespace (and not attached):
##  [1] colorspace_2.0-0       ellipsis_0.3.1         rprojroot_2.0.2       
##  [4] XVector_0.30.0         fs_1.5.0               rstudioapi_0.13       
##  [7] affyio_1.60.0          bit64_4.0.5            fansi_0.4.1           
## [10] AnnotationDbi_1.52.0   lubridate_1.7.9.2      splines_4.0.3         
## [13] geneplotter_1.68.0     knitr_1.30             jsonlite_1.7.1        
## [16] broom_0.7.2            annotate_1.68.0        dbplyr_2.0.0          
## [19] png_0.1-7              BiocManager_1.30.10    compiler_4.0.3        
## [22] httr_1.4.2             backports_1.2.0        assertthat_0.2.1      
## [25] Matrix_1.2-18          lazyeval_0.2.2         cli_2.2.0             
## [28] formatR_1.7            htmltools_0.5.0        tools_4.0.3           
## [31] affy_1.68.0            gtable_0.3.0           glue_1.4.2            
## [34] GenomeInfoDbData_1.2.4 Rcpp_1.0.5             cellranger_1.1.0      
## [37] vctrs_0.3.5            preprocessCore_1.52.0  xfun_0.19             
## [40] testthat_3.0.0         rvest_0.3.6            lifecycle_0.2.0       
## [43] gtools_3.8.2           XML_3.99-0.5           zlibbioc_1.36.0       
## [46] scales_1.1.1           hms_0.5.3              lambda.r_1.2.4        
## [49] yaml_2.2.1             memoise_1.1.0          latticeExtra_0.6-29   
## [52] stringi_1.5.3          RSQLite_2.2.1          highr_0.8             
## [55] genefilter_1.72.0      caTools_1.18.0         BiocParallel_1.24.1   
## [58] rlang_0.4.9            pkgconfig_2.0.3        bitops_1.0-6          
## [61] evaluate_0.14          htmlwidgets_1.5.2      bit_4.0.4             
## [64] tidyselect_1.1.0       R6_2.5.0               generics_0.1.0        
## [67] DelayedArray_0.16.0    DBI_1.1.0              pillar_1.4.7          
## [70] haven_2.3.1            withr_2.3.0            survival_3.2-7        
## [73] RCurl_1.98-1.2         modelr_0.1.8           crayon_1.3.4          
## [76] futile.options_1.0.1   KernSmooth_2.23-18     rmarkdown_2.5         
## [79] jpeg_0.1-8.1           locfit_1.5-9.4         readxl_1.3.1          
## [82] blob_1.2.1             reprex_0.3.0           digest_0.6.27         
## [85] xtable_1.8-4           munsell_0.5.0          viridisLite_0.3.0